Detection of nucleic acids

Abstract

Provided herein is technology relating to detecting and identifying nucleic acids and particularly, but not exclusively, to compositions, methods, kits, and systems for detecting, identifying, and quantifying target nucleic acids with high confidence at single-molecule resolution.

1 - 19 . (canceled) 
     
     
         20 . A system for detecting an analyte in a sample comprising:
 a) a detectably labeled query probe specific for an analyte;   b) a detector configured to detect transient binding of the detectably labeled query probe to said analyte; and   c) a processor configured to:
 i) count the number and/or rate of transient binding events between the detectably labeled query probe and the analyte; and 
 ii) indicate the presence of the analyte in the sample based on the number and/or rate of said transient binding events. 
   
     
     
         21 . The system of  claim 20  wherein said processor is configured to indicate the presence of the analyte in the sample when the number and/or rate of said transient binding events falls within an empirically determined range characteristic of the detectably labeled query probe and the analyte. 
     
     
         22 . The system of  claim 20  wherein said detectably labeled query probe binds to the analyte with a rate constant k on  that is greater than 1 per minute and/or said detectably labeled query probe dissociates from the analyte with a k off  that is greater than 1 per minute. 
     
     
         23 . The system of  claim 20  further comprising an analyte. 
     
     
         24 . The system of  claim 20  further comprising an analyte immobilized to a discrete region of a solid support. 
     
     
         25 . The system of  claim 24  wherein said solid support comprises a microscope slide, a bead, a coverslip, or a cell. 
     
     
         26 . The system of  claim 24  wherein said solid support comprises an immobilized capture probe. 
     
     
         27 . The system of  claim 20  wherein said detectably labeled query probe comprises a fluorescent label. 
     
     
         28 . The system of  claim 20  wherein said processor is configured to produce a kinetic fingerprint characterizing transient binding events between the detectably labeled query probe and the analyte. 
     
     
         29 . The system of  claim 20  wherein said processor is configured to compare the number and/or rate of said transient binding events with the number and/or rate of said transient binding events detected for a positive and/or a negative control. 
     
     
         30 . The system of  claim 20  further comprising a component configured to control the temperature of a sample. 
     
     
         31 . The system of  claim 20  wherein said detectably labeled query probe comprises a nucleic acid. 
     
     
         32 . The system of  claim 20  wherein said detectably labeled query probe comprises a protein. 
     
     
         33 . The system of  claim 20  wherein said processor is configured to apply a statistical treatment to the number and/or rate of transient binding events between the detectably labeled query probe and the analyte. 
     
     
         34 . The system of  claim 20  wherein said processor is configured to apply a Poisson statistical treatment to the number and/or rate of transient binding events between the detectably labeled query probe and the analyte. 
     
     
         35 . The system of  claim 20  wherein said empirically determined range characteristic of the detectably labeled query probe and the analyte is provided by hidden Markov modeling. 
     
     
         36 . The system of  claim 20  wherein said detector detects said transient binding with single-molecule resolution. 
     
     
         37 . The system of  claim 23  further comprising a ligand of said analyte that produces a detectable change in said transient binding of the detectably labeled query probe to said analyte. 
     
     
         38 . The system of  claim 20  further comprising a first analyte and a second analyte. 
     
     
         39 . The system of  claim 38  wherein the processor is configured to distinguish between the first analyte and the second analyte.